Additional file 1 of Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

Additional file 1. Table S1. Field experiments conducted at IRRI, Philippines between the 2014 wet season and 2015 dry season. Table S2. Drought susceptibility index (DSI) calculated for each genotype for the four stress experiments for selected traits (with green for tolerance and red for susceptibility). Table S3. Characterization of the marker set of 215,250 SNPs. Table S4. Significant MTAs detected for ten traits in the population and the gene validation results. Table S5. Yadj. values used for GWAS of the ten traits measured for the 280 diverse set in three environments and two seasons. Table S6. Allelic variation at the GWAS-identified significant loci in the selected 7 accessions for grain yield under lowland and upland drought. Table S7. Details of the 280 diversity panel accessions. Table S8. Description of phenotypic data recording. Figure S1. Projection of 280 lines of the indica-aus diversity panel on the first plane of factorial discriminant analysis using phenotypic data for ten traits. Figure S2. Plots of Pearson’s r-values showing correlation between each of the six experiments (LL_N_WS – lowland non-stress 2014WS, LL_S_DS – lowland non-stress 2015DS, LL_S_WS – lowland stress 2014WS, LL_S_DS – lowland stress 2015DS, UL_S_WS – upland stress 2014WS and UL_S_DS – upland stress 2015DS) at trait level for all the ten phenotypic variables. Figure S3. Heat map showing the uneven marker distribution along each of the 12 chromosomes using the 215,250 SNP working set. Figure S4. Pattern of rapid decay in linkage disequilibrium decay in the population of 280 accessions genotyped with 215,250 SNPs. Figure S5. Circular manhattan plots and qq-plots for each of the 6 experiments and comparison of season-wise analysis to combined analysis for each of the 3 growing environments for a. PL, b. FlgLA, c. BMDW, d. NBP, e. HI, f. TGW and g. SPKFT.